Scientific Report 2008

Molecular Biology

Chairman's Overview

Staff

Peter E. Wright, Ph.D.*
Professor and Chairman
Cecil H. and Ida M. Green Investigator in Medical Research

Ruben Abagyan, Ph.D.
Professor

Carlos F. Barbas III, Ph.D.**
Professor
Janet and W. Keith Kellogg II Chair, Molecular Biology

Rajesh Belani, Ph.D.
Adjunct Assistant Professor
aTyr Pharma
La Jolla, California

Michael N. Boddy, Ph.D.
Assistant Professor

Charles L. Brooks III, Ph.D.***
University of Michigan
Ann Arbor, Michigan

David A. Case, Ph.D.***
Rutgers University
Piscataway, New Jersey

Geoffrey Chang, Ph.D.*
Associate Professor

Eli Chapman, Ph.D.
Assistant Professor of Molecular Biology

Jerold Chun, M.D., Ph.D.
Professor

Lluis Ribas De Pouplana, Ph.D.
Adjunct Assistant Professor
Omnia Molecular
Barcelona, Spain

Ashok Deniz, Ph.D.
Associate Professor

H. Jane Dyson, Ph.D.
Professor

James Arthur Fee, Ph.D.
Professor of Research

Elizabeth D. Getzoff, Ph.D.****
Professor

David B. Goodin, Ph.D.
Associate Professor

David S. Goodsell, Jr., Ph.D.
Associate Professor of Molecular Biology

Joel M. Gottesfeld, Ph.D.
Professor

Jennifer Harris, Ph.D.
Assistant Professor of Biochemistry

Christian A. Hassig, Ph.D.
Adjunct Assistant Professor
Kalypsis, Inc.
San Diego, California

Peter B. Hedlund, M.D., Ph.D.
Assistant Professor of Molecular Biology

John E. Johnson, Ph.D.
Professor

Gerald F. Joyce, M.D., Ph.D.**
Professor
Dean, Faculty

Ehud Keinan, Ph.D.*
Adjunct Professor
Technion-Israel Institute of Technology
Haifa, Israel

Richard A. Lerner, M.D., Ph.D.**
President, The Scripps Research Institute
Lita Annenberg Hazen Professor of Immunochemistry
Cecil H. and Ida M. Green Chair in Chemistry

Scott Lesley, Ph.D.
Assistant Professor of Biochemistry

Tianwei Lin, Ph.D.***
Assistant Professor
University of Hong Kong
Hong Kong, China

Ian MacRae, Ph.D.
Assistant Professor

Clare McGowan, Ph.D.*****
Associate Professor

Duncan E. McRee, Ph.D.
Adjunct Associate Professor
Sorrento Technology
San Diego, California

David P. Millar, Ph.D.
Professor

Louis Noodleman, Ph.D.
Associate Professor

Arthur J. Olson, Ph.D.
Professor

Takanori Otomo, Ph.D.
Assistant Professor

Vijay Reddy, Ph.D.
Associate Professor

Steven I. Reed, Ph.D.*****
Professor

Paul Russell, Ph.D.*****
Professor

Michel Sanner, Ph.D.
Associate Professor

Harold Scheraga, Ph.D.
Adjunct Professor
Cornell University
Ithaca, New York

Paul R. Schimmel, Ph.D.**
Ernest and Jean Hahn Professor of Molecular Biology and Chemistry

Anette Schneemann, Ph.D.
Associate Professor

Subhash C. Sinha, Ph.D.
Associate Professor of Medicinal Chemistry

Gary Siuzdak, Ph.D.
Adjunct Professor
Director, Center for Mass Spectrometry

Vaughn V. Smider, Ph.D.
Assistant Professor of Molecular Biology

Robyn L. Stanfield, Ph.D.
Assistant Professor

Raymond C. Stevens, Ph.D.^†
Professor

Charles D. Stout, Ph.D.
Associate Professor

Peiqing Sun, Ph.D.
Associate Professor

J. Gregor Sutcliffe, Ph.D.
Professor

John A. Tainer, Ph.D.*
Professor

Fujie Tanaka, Ph.D.
Associate Professor

Elizabeth Anne Thomas, Ph.D.
Assistant Professor

James R. Williamson, Ph.D.**
Professor
Dean, Kellogg School of Science and Technology

Ian A. Wilson, D.Phil.*
Professor

Curt Wittenberg, Ph.D.*****
Professor

Kurt Wüthrich, Ph.D.**
Cecil H. and Ida M. Green Professor of Structural Biology

Xiang-Lei Yang, Ph.D.*
Associate Professor of Molecular Biology

Todd O. Yeates, Ph.D.
Adjunct Professor
University of California
Los Angeles, California

Qinghai Zhang, Ph.D.
Assistant Professor

Service Facilities

Gerard Kroon
Manager, Nuclear Magnetic Resonance Facilities

Michael E. Pique
Director, Computer Graphics Development

Senior Staff Scientists

Marc Elsliger, Ph.D.

Quansheng Zhou, Ph.D.

Staff Scientists

Svitlana Berezhna, Ph.D.

Vadim Cherezov, Ph.D.

Reto Horst, Ph.D.

Maria Martinez-Yamout, Ph.D.

Garrett M. Morris, Ph.D.

Chiaki Nishimura, Ph.D.

Jeffrey Speir, Ph.D.

Mutsuo Yamaguchi, Ph.D.

Xueyong Zhu, Ph.D.

Senior Research Associates

Ryan Burnett, Ph.D.***
Tocagen, Inc.
San Diego, California

Adrienne Elizabeth Dubin, Ph.D.

Li Fan, Ph.D.

Maria Alejandra Gamez-Abascal, Ph.D.***
Universidad Autonoma de Madrid
Madrid, Spain

Elsa Garcin, Ph.D.***
University of Maryland
Baltimore, Maryland

Julio Kovacs, Ph.D.***
SeaSpace Corporation
Poway, California

Brent Krueger, Ph.D.***
Hope College
Holland, Michigan

Kelly Lee, Ph.D.

Brian Paegel, Ph.D.

Jefferson Perry, Ph.D.

Richard R. Rivera, Ph.D.

David S. Shin, Ph.D.

Philip Arno Venter, Ph.D.

Xiaoqin Ye, M.D., Ph.D.***
University of Georgia
Athens, Georgia

Research Associates

Melanie Ann Adams, Ph.D.***
University of Toronto
Toronto, Ontario, Canada

Fabio Agnelli, Ph.D.

Hanna-Stina Martinsson Ahlzén, Ph.D.

Reetesh Raj Akhouri, Ph.D.

Alexander Ivanov Alexandrov, Ph.D.***
Takeda
San Diego, California

Stephen G. Aller, Ph.D.

Beatriz Gonzalez Alonso, Ph.D.

Juliano Alves, Ph.D.***
Genomics Institute of the Novartis Research Foundation
San Diego, California

William anderson, Ph.D.

Andrew James Annalora, Ph.D.

Munehito Arai, Ph.D.

Guillermo Asmar-Rovira, Ph.D.

Wojciech Augustyniak, Ph.D.***
Max-Planck Institute
Leipzig, Germany

Sung-Hun Bae, Ph.D.

Krishna Mohan Bajjuri, Ph.D.

Michael Baksh, Ph.D.

Manidipa Banerjee, Ph.D.

Christine Beuck, Ph.D.

David Boehr, Ph.D.

Yannick Bomble, Ph.D.***
National Renewable Energy Laboratory
Golden, Colorado

Giovanni Bottegoni, Ph.D.***
Instituto Italiano de Tecnologia
Genova, Italy

Tommy Bui, Ph.D.

Rosa Maria Cardoso, Ph.D.^††

andrew Barry Carmel, Ph.D.

Juan Jovel Castillo, Ph.D.

Amarnath Chatterjee, Ph.D.

Susana Chaves, Ph.D.^††

Yen-Ju Chen, Ph.D.***
National Synchrotron Radiation Research Center
Hsinchu, Taiwan

Zhiyong Chen, Ph.D.***
Trius Therapeutics
San Diego, California

Srinivas Chittaboina, Ph.D.^††

Ji Woong Choi, Ph.D.

Chung Jen Chou, Ph.D.

Li-Chiou Chuang, Ph.D.^††

Linda Maria Columbus, Ph.D.***
University of Virginia
Charlottesville, Virginia

Stephen Connelly, Ph.D.

Adam Corper, Ph.D.

Sandro Cosconati, Ph.D.***
University of Naples
Naples, Italy

Robert De Bruin, Ph.D.

Pritilekha Deka, Ph.D.

Gerald Edward Dodson, Ph.D.

Claire Louise Dovey, Ph.D.

Jerome Dupuy, Ph.D.***
Université Mediterranée
Marseille, France

Michelle Duquette-Huber, Ph.D.

Stephen Edgcomb, Ph.D.

Susanna V. Ekholm-Reed, Ph.D.

Venkata Reddy Erigala, Ph.D.

Daniel Felitsky, Ph.D.

Allan Chris Merrera Ferreon, Ph.D.

Josephine Chu Ferreon, Ph.D.

Stefano Forli, Ph.D.

Chi-Yu Fu, Ph.D.

Zara Fulton, Ph.D.

Yann Gambin, Ph.D.

Julia Gavrilyuk, Ph.D.

Charles Gersbach, Ph.D.

Joshua Gill, Ph.D.

Edith Caroline Glazer, Ph.D.

Rajib Kumar Goswami, Ph.D.

Arsen Grigoryan, Ph.D.

Bettina Groschel, Ph.D.***
Ardea Biosciences, Inc.
San Diego, California

Hai-Ming Guo, Ph.D.***
Hanan Normal University
Hanan, China

Min Guo, Ph.D.

Rey-Ting Guo, Ph.D.

Mahender Gurram, Ph.D.***
AMRI
Albany, New York

Peter Haberz, Ph.D.

Byung Woo Han, Ph.D.

Rodney Harris, Ph.D.

David M. Herman, Ph.D.

Deron Herr, Ph.D.

Kenichi Hitomi, Ph.D.

Minsun Hong, Ph.D.

Wen-Xu Hong, Ph.D.

Fang Hu, Ph.D.

Veli-Pekka Jaakola, Ph.D.

Thamara Janaratne, Ph.D.

Christine Jespersen, Ph.D.

Margaret Alice Johnson, Ph.D.

Steven Johnson, Ph.D.

Susanna Juraja, Ph.D.

Sachin Kale, Ph.D.

Tse Siang Kang, Ph.D.

Mili Kapoor, Ph.D.

Ananta Karmakar, Ph.D.

Andrey Aleksandrovich Karyakin, Ph.D.

Donald Keidel, Ph.D.

Reza Khayat, Ph.D.

Dae Hee Kim, Ph.D.

Eda Koculi, Ph.D.^††

Bethany Koehntop, Ph.D.

Irina Kufareva, Ph.D.

Sharon Kwan, Ph.D.

Bianca Lam, Ph.D.

Petra Langerak, Ph.D.

Emma Langley, Ph.D.^††

Jason Lanman, Ph.D.

Joachim Latzer, Ph.D.

Chang-Wook Lee, Ph.D.

Chul Won Lee, Ph.D.

Young-Tae Lee, Ph.D.

Sophie Lefebvre, Ph.D.^††

Edward Lemke, Ph.D.

Vasco Liberal, Ph.D.***
Alert Life Sciences Computing
Villa Novade Gaia, Portugal

William M. Lindstrom, Ph.D.***
Acelot, Inc.
Santa Barbara, California

Bin Liu, Ph.D.

Hsiao-Wei Liu, Ph.D.

Wei Liu, Ph.D.

Kunheng Luo, Ph.D.

Darly Joseph Manayani, Ph.D.***
Pax Vax
San Diego, California

Santiago Cavero Martinez, Ph.D.^††

Tsutomu Matsui, Ph.D.

Derrick Meinhold, Ph.D.

Eva Mejia Ramirez De Arellano, Ph.D.

Elena Menichelli, Ph.D.

Andrew Mercer, Ph.D.

Jonathan Mikolosko, Ph.D.

Mauro Mileni, Ph.D.

Maki Minakawa, Ph.D.***
Riken, Wako Institute
Saitama, Japan

Satoshi Mizuta, Ph.D.

Biswaranjan Mohanty, Ph.D.

Davide Moiani, Ph.D.

Samrat Mukhopadhyay, Ph.D.

Tetsuji Mutoh, Ph.D.

Mir Hussain Nawaz, Ph.D.

Tuan Nguyen, Ph.D.

George Nicola, Ph.D.

Kyoko Noguchi, M.D., Ph.D.

Wataru Nomura, Ph.D.***
Tokyo Medical and Dental University
Tokyo, Japan

Amy Odegard, Ph.D.

Akira Onoda, Ph.D.***
Osaka University

Osaka, Japan

So-Jung Park, Ph.D.

Sung-Jean Park, Ph.D.

Stephanie Pebernard, Ph.D.^††

Bill Francesco Pedrini, Ph.D.***
ETH Zurich
Zürich, Switzerland

Robert Pejchal, Ph.D.

Vladimir Pelmenschikov, Ph.D.***
Vrije Universiteit
Amsterdam, the Netherlands

Alexander Perryman, Ph.D.

Suzanne Peterson, Ph.D.

Jessica Petrillo, Ph.D.***
office of Chemical and Biological Weapons, Threat Reduction
Washington, D.C.

Ron Piran, Ph.D.

William Placzek, Ph.D.***
Burnham Institute for Medical Research
La Jolla, California

Goran Pljevalj?ci?Lc, Ph.D.

Stephanie Pond, Ph.D.***
Prognosys Biosciences, Inc.
La Jolla, California

John Prudden, Ph.D.

Kimberly A. Reynolds, Ph.D.***
University of Texas
Dallas, Texas

Jin-Kyu Rhee, Ph.D.***
Department of Chemistry, Scripps Research

Errin Rider, Ph.D.

Gabriela Ring, Ph.D.

Rae Robertson, Ph.D.

Christopher Roth, Ph.D.

Manuel Rueda, Ph.D.

Mariana Santa-Marta, Ph.D.

Gor Sarkisyan, Ph.D.

Alim Seit-Nebi, Ph.D.^††

Riturparna Sinha Roy, Ph.D.***
Brigham and Women's Hospital
Boston, Massachusetts

andre Schiefner, Ph.D.

Lauren J. Schwimmer, Ph.D.^††

Jennifer S. Scorah, Ph.D.***
CovX
La Jolla, California

Pedro Serrano-Navarro, Ph.D.

Zahra Shajani, Ph.D.

David A. Shore, Ph.D.

Daniela andrea Slavin, Ph.D.***
Ligand Pharmaceuticals
San Diego, California

Elisabetta Soragni, Ph.D.

Surya Venkata Sripada, Ph.D.***
Syngene International, Ltd.
Bangalore, India

Pawel Stanczak, Ph.D.

Thomas Steinbrecher, Ph.D.

Pal Stenmark, Ph.D.***
Karolinska Institutet
Stockholm, Sweden

Shih-Che Su, Ph.D.

Sebastian Sudek, Ph.D.

Salahuddin Syed, Ph.D.

Michael T. Sykes, Ph.D.

Blair R. Szymczyna, Ph.D.

Bin Tang, Ph.D.

Rebecca E. Taurog, Ph.D.

Ewan Richardson Taylor, Ph.D.

Leonardo Teixeira, Ph.D.

Mauricio Carrillo Tripp, Ph.D.

Oleg Trott, Ph.D

Ulrich Tschulena, Ph.D.***
German Cancer Research Center
Heidelberg, Germany

Julie L. Tubbs, Ph.D.

Hisatoshi Uehara, Ph.D.

Naoto Utsumi, Ph.D.***
Otsuka Pharmaceutical Co., Ltd.
Tokushima, Japan

Ajay Vashisht, Ph.D.***
University of California
Los Angeles, California

Sangita Venkataraman, Ph.D.

Petra Verdino, Ph.D.

My Vo, Ph.D.

Jun Wang, Ph.D.

Jessica Williams, Ph.D.

Robert Scott Williams, Ph.D.

Vance Wong, Ph.D.

Ulrich Wuellner, Ph.D.

Wei Xie, Ph.D.***
Salk Institute for Biological Studies
La Jolla, California

Chunping Xu, Ph.D.

Rui Xu, Ph.D.

Yoshiki Yamada, Ph.D.^††

Tohru Yamagaki, Ph.D.***
Suntory Institute for Bioorganic Research
Osaka, Japan

Kye Sook Yi, Ph.D.

Sung-Il Yoon, Ph.D.

Naoto Yoshizuka, M.D., Ph.D.

Haile Zhang, Ph.D.

Qing Zhang, Ph.D.***
Glaxo Smith Kline

Shanghai, China

Wei Zhang, Ph.D.***
aTyr Pharma
La Jolla, California

Qiang Zhao, Ph.D.

Yong Zhao, Ph.D.***
Cambridge Soft
Cambridge, Massachusetts

Scientific Associates

Enrique Abola, Ph.D.

andrew S. Arvai, M.S.

Dennis Carlton, B.S.

Ellen Yu-Lin Tsai Chien, Ph.D.

Xiaoping Dai, Ph.D.

Marc Deller, D.Phil.

Gye Won Han, Ph.D.

Wenge Han, Ph.D.

Michael Allen Hanson, Ph.D.

Hope Johnson, Ph.D.***
California State University
Fullerton, California

Teresa Jones, Ph.D.

Lin Wang, Ph.D.***
MedImmune, L.L.C.
Gaithersburg, Maryland

Visiting Investigators

Stephen J. Benkovic, Ph.D.
Pennsylvania State University
University Park, Pennsylvania

Tobias Cramer, Ph.D.
CINECA Supercomputer Center HPC Europe
Bologna, Italy

Tammy Dwyer, Ph.D.
San Diego State University
San Diego, California

Wayne A. Fenton, Ph.D.
Yale University
New Haven, Connecticut

Astrid Graslund, Ph.D.
Stockholm University
Stockholm, Sweden

Arne Holmgren, M.D., Ph.D.
Karolinska Institutet
Stockholm, Sweden

Barry Honig, Ph.D.
Columbia University
New York, New York

Arthur Horwich, M.D.
Yale University
New Haven, Connecticut

Tai-Huang Huang, Ph.D.
Academica Sinica
Taipei, Taiwan

Michael Johnson, Ph.D.
University of Chicago
Chicago, Illinois

Joseph David Ng, Ph.D.
University of Alabama
Huntsville, Alabama

Mary Jo Ondrechen, Ph.D.
Northeastern University
Boston, Massachusetts

Victoria A. Roberts, Ph.D.
University of California
San Diego, California

Robert D. Rosenstein, Ph.D.
Lawrence Berkeley National Laboratory
Berkeley, California

^†† Appointment completed